One interesting thing to consider is a lot of the catastrophic magazine detonations mentioned above were due to those ships using two part ammo, a shell and a charge. I was looking up magazine detonations to try and abstract it in a way that would fit Aurora as missiles are a single unit. I did find some things on smaller ships that had their magazines detonate such as destroyers in the Pacific, these use self contained shells which people are more familiar with (single unit ammunition). In pretty much all cases I found this resulted in the loss of the ship. The only real exception I could find was during the attack on Pearl Harbor. The USS Shaw took a hit and had its forward magazine detonate while in dry dock, they ended up having to replace the entire Bow of the ship. Another thing to note is that the most common cause of a magazine detonation was fire rather than a direct hit. While it would be neat to see fires and their effect on crews (I would love to be able to recover and press burnt out hulk back into service) I'm not sure how well it would fit in Aurora (although I could've swore Ive seen something for this in the VB Aurora database).
Another angle to approach this from in terms of ammunition detonation would be in Tanks. A few modern tanks have blow out panels which allow the force of a magazine detonation to be mitigated. These blow off panels allow energy to escape rather than keeping it bottled up and causing more catastrophic damage to the vehicle. Instead of outright ejecting ordinance could a system where the damage is basically vented off be a better hand wave? Would this dump the damage outright or would it be more of a mitigation? Could this be simple damage mitigation (Y% chance of X% of damage is vented into space) for low tech magazines and better chances for partial or even total mitigation of damage? Would this cause the ships thermal signature to skyrocket? I feel something along these lines would provide more variance rather than the all or nothing approach we have now. It would also still allow for big explosions (ask me about my deep magazines, combat colliers, and large numbers!) and allow the player to mitigate or stop this damage by design/tech.
As for the whole "Nukes don't set off other nukes" thing, maybe TN elements integrated into warhead designs do
too good of a job at turning energy into neutrons.